I'd like to keep it where I'm just dealing with cops, but if feds get involved, I'm Wondering how many and for how long.
Why are Feds getting involved? Oh yeah, because you're writing them in. Simple solution -- Don't write them in.
The FBI investigates on certain types of crimes. They don't get involved in local stuff, though they can always be consulted. FBI deals with Federal cases and Federal crimes.
Serial killers are one of their types of investigations and every local jurisdiction will call them in for help if they suspect one. The FBI has the data, background and resources to investigate these. But your child is simply a run-away as far as your description goes.
The FBI would already be working the serial killer case and, as part of that, monitoring any disappearances in the area. But they would be working to a profile and the missing kid would just be data entered into their systems unless they have a reason to expect otherwise.
At any rate, you can write the story from the local agency's perspective, bringing in the FBI as it fits your story. Without knowing the story, nobody can give you any specific answers to your questions.
Again, what do you need to happen for your story to work?
Jeff